For ten days across recent summers, researchers aboard the University of Delaware research vessel Hugh R. Sharp collected water samples from the mouth of the Susquehanna River to Solomons Island in a first-of-its-kind investigation. They wanted to know when and where the waters of the Chesapeake Bay were turning most acidic.

One finding: As oceans around the world absorb carbon dioxide and acidify, the changes are likely to come faster to the nation's largest estuary.

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Scientists have long studied the slow and steady acidification of the open oceans — and its negative effects. Acidifying waters can kill coral, disrupt oyster reproduction, dissolve snail shells like nails in a can of bubbly Coke.

But researchers are just beginning to investigate the consequences for the Chesapeake. And they're finding that acidification could compound the ecological challenges already wracking the bay.

Not all effects are immediately negative on all species. Experiments are showing that blue crabs, marsh grasses and algae could theoretically thrive in the conditions expected to develop over the next century. But the acidification is a threat to other keystone bay species, such as oysters — a key source of food for crabs. Scientists say acidification could dramatically and unpredictably alter the delicate balances that stabilize the bay ecosystem.

With so many variables expected to affect bay creatures — including rising acidity, warming waters and continued nutrient pollution — research is complex.

The Smithsonian Environmental Research Center has a wetland where it is studying the impacts of increased carbon dioxide levels in bay waters on the aquatic ecosystem. (Lloyd Fox / Baltimore Sun)

"When you have three things changing at once, that's where our challenges really increase," said Jeff Cornwell, a research professor at the University of Maryland Center for Environmental Science in Cambridge. "All these things are intertwined."

Water, as they teach in middle school chemistry, has a neutral pH of 7. But over the past 300 million years or so, ocean water has registered as basic, with an average pH of 8.2.

As carbon dioxide has multiplied in the atmosphere over the past century, it has also dissolved into the oceans, producing carbonic acid. That has dropped ocean pH to 8.1. The shift might seem slight, but it actually represents a 30 percent increase in acidity, because the pH scale is logarithmic.

The consequences, coupled with the impacts of rising ocean temperatures, could eventually be severe. Research suggests that the acidity that could develop by 2100 could make it harder for oysters, clams, sea urchins and corals to build their protective shells, and could even dissolve the shell of the pea-sized creature at the base of the food web known as a sea butterfly.

But that's just in the open ocean. Most research focuses on that massive habitat, because its chemistry is largely consistent from one spot to another. In environments close to land, where ecology is more complex and active, biological processes like photosynthesis and respiration drive more volatile swings in acidity and other chemistry.

Whitman Miller is a research scientist at the Smithsonian Environmental Research Center in Edgewater.

If an acidifying ocean is like a bottle of carbonated seltzer water, he said, estuaries like the Chesapeake are similar to a beer.

"Because it's so uniform, in some ways, we know much more about the open ocean at the global scale than we do these local scales we're tangling with in estuaries," he said.

Researchers around Maryland and across the country are working to bridge that knowledge gap.

Research published last month in the journal Nature Communications showed that acidification is already apparent in the bay. The team that measured acidity across the bay, led by the University of Delaware marine science professor Wei-Jun Cai, found a zone of increasing acidity at depths of about 30 to 50 feet across the Chesapeake. While surface waters hover around the pH norm of 8.2, the deeper waters registered almost one point lower — nearly 10 times more acidic.

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The researchers, who included Cornwell and colleagues from UMCES, believe it's not only the global effects of carbon dioxide emissions, but also the dead zones of low or no oxygen that have plagued the bay for decades. The zones are created when nitrogen and phosphorus runoff from farms, lawns and sewage fertilize large algae blooms. Microbes strip oxygen from the water to decompose the blooms when they die, and release more carbon dioxide in the process.

The problem is worsened when organic matter is decomposed in water that is already stripped of oxygen — the bacteria use up other compounds in the water that produce an acidic chemical, hydrogen sulfide. Hydrogen sulfide is what makes the muck around the bay smell like rotten eggs.

Cai said the processes suggest that the bay, and other waterways struggling to reduce nutrient loads, are especially vulnerable as the pH of waters around the globe decline.

"You have something we call a synergistic effect, where one plus one gives you something more than two," he said. "There's a very strong acidification effect."

Miller and colleagues at the Smithsonian are exploring the consequences in a meadow of marsh that looks like so many others around the Chesapeake — except this one is dotted with metal heat lamps and plexiglass chambers that are helping to simulate the environment of the future. They call it the Global Change Research Wetland.

Scientists are conducting experiments to study the effects of increasing carbon dioxide, nutrients and temperature on the growth of sedge grasses and invasive plants, and the ability of the Rhode River marsh to grow upward to match sea level rise.

One study has been running for 30 years. Pat Megonigal, a biogeochemist and lead investigator of the research wetland, says it should be listed in the Guinness Book of World Records for the longest-running climate change experiment.

Along the creek that flows into the marsh, researchers from the Smithsonian Institution have built a gateway through which they are measuring the carbon content of water as it flows in and out twice a day with the tides. Some of it is carbon dioxide, but a portion is the compounds carbonate and bicarbonate — elements that may actually help counteract acidification in the estuary.

They hope the data will help explain not only what changes acidification could bring, but also what role natural ecological processes could play in limiting them.

"It tells us something about the influence of the marsh on the chemistry of the water," Megonigal said. "We think the net effect of water leaving the marsh is to buffer the acidity of the estuary."

Other researchers are eagerly testing what those changes could mean for the bay's crabs and oysters.

For her recently completed dissertation, UMCES doctoral candidate Hillary Glandon exposed blue crabs to both warmer and more acidic waters and watched their response. She found that acidification alone didn't affect them, but when it was coupled with warmer waters, crabs grew faster, molting old shells more frequently, and they also ate more food.

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Previous research has already shown that oysters, mussels and similar shellfish could struggle in acidifying waters. They build their shells out of a compound in the water known as calcium carbonate, and scientists have found there will be less of those building blocks available as ocean carbon dioxide levels rise.

So Glandon's colleagues Cornwell and Jeremy Testa are investigating what that could mean for restoration of the Chesapeake Bay's oysters. They're getting input from researchers in Oregon, where acidification has already challenged aquaculture efforts by killing oyster larvae. Though they don't expect the exact same conditions in the bay, they are watching pH levels closely in places such as Harris Creek, one of three Choptank River tributaries where millions of dollars have been spent on building and seeding new reefs.

Any changes could throw off a complex food web. While crabs could be thriving in warmer and more acidic bay waters in the future, the oysters and mussels they eat could be struggling.

"Crabs don't exist in a vacuum," Glandon said. "If food they're going to be eating is less abundant, there may be negative effects."

Tom Miller, director of UMCES' Chesapeake Biological Laboratory in Solomons, said the stakes demand that more resources be put into measuring and understanding acidification. In the same way state and federal officials have tried to limit pollution to protect crabs, oysters, marshes and underwater grasses, he said, acidification should be getting more attention in bay policy discussions.

"It has the potential to fundamentally change the pattern, the seasonality and the location of fishing in a way that the grandfathers of today's watermen wouldn't recognize," he said. "We should be having those discussions now — not in 20 years or so, when it becomes, I wouldn't say too late, but when it becomes much more contentious."